1
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Hilditch AT, Romanyuk A, Hodgson LR, Mantell J, Neal CR, Verkade P, Obexer R, Serpell LC, McManus JJ, Woolfson DN. Maturation and Conformational Switching of a De Novo Designed Phase-Separating Polypeptide. J Am Chem Soc 2024; 146:10240-10245. [PMID: 38578222 PMCID: PMC11027135 DOI: 10.1021/jacs.4c00256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/06/2024]
Abstract
Cellular compartments formed by biomolecular condensation are widespread features of cell biology. These organelle-like assemblies compartmentalize macromolecules dynamically within the crowded intracellular environment. However, the intermolecular interactions that produce condensed droplets may also create arrested states and potentially pathological assemblies such as fibers, aggregates, and gels through droplet maturation. Protein liquid-liquid phase separation is a metastable process, so maturation may be an intrinsic property of phase-separating proteins, where nucleation of different phases or states arises in supersaturated condensates. Here, we describe the formation of both phase-separated droplets and proteinaceous fibers driven by a de novo designed polypeptide. We characterize the formation of supramolecular fibers in vitro and in bacterial cells. We show that client proteins can be targeted to the fibers in cells using a droplet-forming construct. Finally, we explore the interplay between phase separation and fiber formation of the de novo polypeptide, showing that the droplets mature with a post-translational switch to largely β conformations, analogous to models of pathological phase separation.
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Affiliation(s)
- Alexander T. Hilditch
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
- Max
Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Andrey Romanyuk
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
- Max
Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Lorna R. Hodgson
- Wolfson
Bioimaging Facility, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K.
| | - Judith Mantell
- Wolfson
Bioimaging Facility, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K.
| | - Christopher R. Neal
- Wolfson
Bioimaging Facility, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K.
| | - Paul Verkade
- School
of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K.
- Bristol
BioDesign Institute, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Richard Obexer
- Department
of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, U.K.
| | - Louise C. Serpell
- School
of Life Sciences, University of Sussex, Falmer, Brighton, JMS 3B17, U.K.
| | - Jennifer J. McManus
- Bristol
BioDesign Institute, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
- HH Wills
Physics Laboratory, School of Physics, University
of Bristol, Tyndall Avenue, Bristol BS8 1TL, U.K.
| | - Derek N. Woolfson
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
- Max
Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
- School
of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K.
- Bristol
BioDesign Institute, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
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2
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Lopez JG, Hein Y, Erez A. Grow now, pay later: When should a bacterium go into debt? Proc Natl Acad Sci U S A 2024; 121:e2314900121. [PMID: 38588417 PMCID: PMC11032434 DOI: 10.1073/pnas.2314900121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 03/03/2024] [Indexed: 04/10/2024] Open
Abstract
Microbes grow in a wide variety of environments and must balance growth and stress resistance. Despite the prevalence of such trade-offs, understanding of their role in nonsteady environments is limited. In this study, we introduce a mathematical model of "growth debt," where microbes grow rapidly initially, paying later with slower growth or heightened mortality. We first compare our model to a classical chemostat experiment, validating our proposed dynamics and quantifying Escherichia coli's stress resistance dynamics. Extending the chemostat theory to include serial-dilution cultures, we derive phase diagrams for the persistence of "debtor" microbes. We find that debtors cannot coexist with nondebtors if "payment" is increased mortality but can coexist if it lowers enzyme affinity. Surprisingly, weak noise considerably extends the persistence of resistance elements, pertinent for antibiotic resistance management. Our microbial debt theory, broadly applicable across many environments, bridges the gap between chemostat and serial dilution systems.
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Affiliation(s)
- Jaime G. Lopez
- Department of Bioengineering, Stanford University, Stanford, CA94305
- Racah Institute of Physics, The Hebrew University, Jerusalem9190401, Israel
- Department of Applied Physics, Stanford University, Stanford, CA94305
| | - Yaïr Hein
- Institute for Theoretical Physics, Utrecht University, Utrecht3584 CC, Netherlands
| | - Amir Erez
- Racah Institute of Physics, The Hebrew University, Jerusalem9190401, Israel
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3
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Shang XY, Xu C, Chen FX. From snapshots to a movie: Capturing eukaryotic transcription initiation at single-nucleotide resolution. Sci Bull (Beijing) 2024; 69:853-855. [PMID: 38320900 DOI: 10.1016/j.scib.2024.01.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Affiliation(s)
- Xue-Ying Shang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Radiation Oncology, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Congling Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Radiation Oncology, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China; Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
| | - Fei Xavier Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Radiation Oncology, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
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4
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Tian H, Rajbhandari P, Tarolli J, Decker AM, Neelakantan TV, Angerer T, Zandkarimi F, Remotti H, Frache G, Winograd N, Stockwell BR. Multimodal mass spectrometry imaging identifies cell-type-specific metabolic and lipidomic variation in the mammalian liver. Dev Cell 2024; 59:869-881.e6. [PMID: 38359832 DOI: 10.1016/j.devcel.2024.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 05/11/2023] [Accepted: 01/26/2024] [Indexed: 02/17/2024]
Abstract
Spatial single-cell omics provides a readout of biochemical processes. It is challenging to capture the transient lipidome/metabolome from cells in a native tissue environment. We employed water gas cluster ion beam secondary ion mass spectrometry imaging ([H2O]n>28K-GCIB-SIMS) at ≤3 μm resolution using a cryogenic imaging workflow. This allowed multiple biomolecular imaging modes on the near-native-state liver at single-cell resolution. Our workflow utilizes desorption electrospray ionization (DESI) to build a reference map of metabolic heterogeneity and zonation across liver functional units at tissue level. Cryogenic dual-SIMS integrated metabolomics, lipidomics, and proteomics in the same liver lobules at single-cell level, characterizing the cellular landscape and metabolic states in different cell types. Lipids and metabolites classified liver metabolic zones, cell types and subtypes, highlighting the power of spatial multi-omics at high spatial resolution for understanding celluar and biomolecular organizations in the mammalian liver.
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Affiliation(s)
- Hua Tian
- Environmental and Occupational Health, Pitt Public Health, Pittsburgh, PA 15261, USA; Children's Neuroscience Institute, School of Medicine, Pittsburgh, PA 15224, USA.
| | - Presha Rajbhandari
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | | | - Aubrianna M Decker
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | | | - Tina Angerer
- The Luxembourg Institute of Science and Technology, 4362 Esch-sur-Alzette, Luxembourg; Department of Pharmaceutical Biosciences, Uppsala University, 751 05 Uppsala, Sweden
| | | | - Helen Remotti
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Gilles Frache
- The Luxembourg Institute of Science and Technology, 4362 Esch-sur-Alzette, Luxembourg
| | - Nicholas Winograd
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Brent R Stockwell
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Chemistry, Columbia University, New York, NY 10027, USA; Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA.
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5
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Mehrotra A, Busch AB, Uscher-Pines L, Raja P, Huskamp HA. In-Person Visits Before Initiation of Telemedicine for Mental Illness. JAMA Health Forum 2024; 5:e240234. [PMID: 38578629 PMCID: PMC10998149 DOI: 10.1001/jamahealthforum.2024.0234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/24/2024] [Indexed: 04/06/2024] Open
Abstract
This cross-sectional study examines how often patients had an in-person visit before initiating telemedicine for mental illness between 2019 and 2022.
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Affiliation(s)
- Ateev Mehrotra
- Department of Health Care Policy, Harvard Medical School, Boston, Massachusetts
- Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Alisa B. Busch
- Department of Health Care Policy, Harvard Medical School, Boston, Massachusetts
- McLean Hospital, Belmont, Massachusetts
| | | | - Pushpa Raja
- Greater Los Angeles Veterans Affairs Medical Center, Los Angeles, California
| | - Haiden A. Huskamp
- Department of Health Care Policy, Harvard Medical School, Boston, Massachusetts
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6
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Nikeleit V, Roth L, Maisch M, Kappler A, Bryce C. Phototrophic Fe(II) oxidation benefits from light/dark cycles. Environ Microbiol Rep 2024; 16:e13239. [PMID: 38490970 PMCID: PMC10943175 DOI: 10.1111/1758-2229.13239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 02/01/2024] [Indexed: 03/18/2024]
Abstract
Phototrophic Fe(II)-oxidizers use Fe(II) as electron donor for CO2 fixation thus linking Fe(II) oxidation, ATP formation, and growth directly to the availability of sunlight. We compared the effect of short (10 h light/14 h dark) and long (2-3 days light/2-3 days dark) light/dark cycles to constant light conditions for the phototrophic Fe(II)-oxidizer Chlorobium ferrooxidans KoFox. Fe(II) oxidation was completed first in the setup with constant light (9 mM Fe(II) oxidised within 8.9 days) compared to the light/dark cycles but both short and long light/dark cycles showed faster maximum Fe(II) oxidation rates. In the short and long cycle, Fe(II) oxidation rates reached 3.5 ± 1.0 and 2.6 ± 0.3 mM/d, respectively, compared to 2.1 ± 0.3 mM/d in the constant light setup. Maximum Fe(II) oxidation was significantly faster in the short cycle compared to the constant light setup. Cell growth reached roughly equivalent cell numbers across all three light conditions (from 0.2-2.0 × 106 cells/mL to 1.1-1.4 × 108 cells/mL) and took place in both the light and dark phases of incubation. SEM images showed different mineral structures independent of the light setup and 57 Fe Mössbauer spectroscopy confirmed the formation of poorly crystalline Fe(III) oxyhydroxides (such as ferrihydrite) in all three setups. Our results suggest that periods of darkness have a significant impact on phototrophic Fe(II)-oxidizers and significantly influence rates of Fe(II) oxidation.
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Affiliation(s)
- Verena Nikeleit
- Department of GeosciencesUniversity of TübingenTübingenGermany
| | - Linda Roth
- Department of GeosciencesUniversity of TübingenTübingenGermany
| | - Markus Maisch
- Department of GeosciencesUniversity of TübingenTübingenGermany
| | - Andreas Kappler
- Department of GeosciencesUniversity of TübingenTübingenGermany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight InfectionsTübingenGermany
| | - Casey Bryce
- School of Earth SciencesUniversity of BristolBristolUK
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7
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Wang T, Zhou Y. A PASS for protein secretion. Nat Chem Biol 2024; 20:396-398. [PMID: 37872401 DOI: 10.1038/s41589-023-01444-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Affiliation(s)
- Tianlu Wang
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
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8
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Schug A. Residue coevolution and mutational landscape for OmpR and NarL: You can teach old dogs new tricks. Biophys J 2024; 123:653-654. [PMID: 38379283 PMCID: PMC10995386 DOI: 10.1016/j.bpj.2024.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 02/22/2024] Open
Affiliation(s)
- Alexander Schug
- Jülich Supercomputing Centre, Forschungszentrum Jülich, Jülich, Germany; Faculty of Biology, University of Duisburg-Essen, Essen, Germany.
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9
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Zhang J, Fei C, Qi S, Fu J, Zhou S, Wang Z, Li J, Zhao Y, Wu D. The toxicity response of the electrochemical signal of the cell to the drug metabolized by the S9 system. Analyst 2024; 149:1921-1928. [PMID: 38375539 DOI: 10.1039/d4an00010b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
The electrochemical detection method of cytotoxicity using intracellular purines as biomarkers has shown great potential for in vitro drug toxicity evaluation. However, no electrochemical detection system based on an in vitro drug metabolism mechanism has been devised. In this paper, electrochemical voltammetry was used to investigate the effect of the S9 system on the electrochemical behavior of HepG2 cells, and benzo[a]pyrene, fluoranthene, and pyrene were employed to investigate the sensitivity of electrochemical signals of cells to the cytotoxicity of drugs metabolized by the S9 system. The results showed that, within 8 h of exposure to the S9 system, the electrochemical signal of HepG2 cells at 0.7 V did not alter noticeably. The levels of xanthine, guanine, hypoxanthine, and adenine in the cells were not significantly altered. Compared with the absence of S9 system metabolism, benzo[a]pyrene and fluoranthene processed by the S9 system decreased the electrochemical signal of the cells in a dose-dependent manner, while pyrene did not change it appreciably. HPLC also revealed that benzo[a]pyrene and fluoranthene metabolized by the S9 system decreased the intracellular purine levels, whereas pyrene had no effect on them before and after S9 system metabolism. The cytotoxicity results of the three drugs examined by electrochemical voltammetry and MTT assay showed a strong correlation and good agreement. The S9 system had no effect on the intracellular purine levels or the electrochemical signal of cells. When the drug was metabolized by the S9 system, variations in cytotoxicity could be precisely detected by electrochemical voltammetry.
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Affiliation(s)
- Jiahuan Zhang
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, P. R. China.
- Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi 154007, China
| | - Chaoqun Fei
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, P. R. China.
| | - Shulan Qi
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, P. R. China.
| | - Jiaqi Fu
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, P. R. China.
| | - Shi Zhou
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, P. R. China.
- Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi 154007, China
| | - Zhong Wang
- Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi 154007, China
- College of Biology and Agriculture, Jiamusi University, Jiamusi, Heilongjiang 154007, P. R. China
| | - Jinlian Li
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, P. R. China.
- Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi 154007, China
| | - Yanli Zhao
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, P. R. China.
- Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi 154007, China
| | - Dongmei Wu
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang 154007, P. R. China.
- Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi University, Jiamusi 154007, China
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10
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Mahase E. HIV: WHO reports "worrying" increase in resistance to key antiretroviral treatment. BMJ 2024; 384:q573. [PMID: 38448055 DOI: 10.1136/bmj.q573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
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11
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Bartley JM, Xu M. Unleashing CAR T cells to delay metabolic aging. Nat Aging 2024; 4:284-286. [PMID: 38360926 PMCID: PMC11074700 DOI: 10.1038/s43587-024-00576-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Amor and colleagues previously developed chimeric antigen receptor (CAR) T cells that can target and eliminate senescent cells. The utility of these senolytic CAR T cells is now expanded to show that they can combat age-related metabolic dysfunction, and that they can be used prophylactically and have effects that persist for months, thus opening the door to the development of long-term senolytic approaches.
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Affiliation(s)
- Jenna M Bartley
- UConn Center on Aging, UConn Health, Farmington, CT, USA.
- Department of Immunology, UConn Health, Farmington, CT, USA.
| | - Ming Xu
- UConn Center on Aging, UConn Health, Farmington, CT, USA.
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA.
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12
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Çakir S. Effect of Boric Acid on Metabolic Peptides and Some Biochemical Parameters in Experimental Diabetic Rats. Biol Trace Elem Res 2024; 202:1001-1008. [PMID: 37872360 DOI: 10.1007/s12011-023-03910-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/06/2023] [Indexed: 10/25/2023]
Abstract
Boron (B) is an element that has recently been wondered and researched in many fields, especially due to its effects on energy metabolism. The aim of this study is to evaluate the effect of boric acid (BA) on newly discovered energy metabolism peptides that have not been studied before. In this study, the effects of 15 mg/kg of BA were evaluated in 24 Wistar rats. Groups were named as control group, 15 mg/kg BA group, streptozotocin (STZ)-induced experimental diabetic group, and STZ-induced experimental diabetic + 15 mg/kg BA administered group (STZ+15 mg/kg BA). Serum asprosin, nesfatin-1, preptin, insulin, total cholesterol (TC), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), aspartate transaminase (AST), alanine transaminase (ALT), and glucose analyses were performed. In this study, the increase in glucose, TG, TC, LDL-C levels, and AST, ALT activities in STZ-induced groups were reduced with BA administration. While HDL-C level significantly decreased in the STZ group, the level approached the control group values after BA administration (p<0.001). As for peptides, although there was a statistically significant increase after 15 mg/kg BA administration, these levels did not approach the control group values (p<0.001). According to the findings, STZ-induced diabetes mellitus and the biochemical processes that develop accordingly change correlatively. This study showed that BA is effective in energy metabolism.
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Affiliation(s)
- Selcen Çakir
- Department of Medical Services and Techniques, Medical Laboratory Techniques Program, Vocational School of Health Services, Çanakkale, Turkey.
- Vocational School of Health Services, Çanakkale Onsekiz Mart University, Terzioğlu Campus, SHMYO Z-9. PK:17000, Çanakkale, Turkey.
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13
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Lanctot A. A high-yielding recipe: Cytokinin signaling in soybean roots affects phosphorus uptake efficiency and crop production. Plant Physiol 2024; 194:1260-1262. [PMID: 37976166 PMCID: PMC10904338 DOI: 10.1093/plphys/kiad616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Affiliation(s)
- Amy Lanctot
- Assistant Features Editor, Plant Physiology, American Society of Plant Biologists
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA 11724
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14
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Machado D. A benchmark of optimization solvers for genome-scale metabolic modeling of organisms and communities. mSystems 2024; 9:e0083323. [PMID: 38251879 PMCID: PMC10878033 DOI: 10.1128/msystems.00833-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Genome-scale metabolic modeling is a powerful framework for predicting metabolic phenotypes of any organism with an annotated genome. For two decades, this framework has been used for the rational design of microbial cell factories. In the last decade, the range of applications has exploded, and new frontiers have emerged, including the study of the gut microbiome and its health implications and the role of microbial communities in global ecosystems. However, all the critical steps in this framework, from model construction to simulation, require the use of powerful linear optimization solvers, with the choice often relying on commercial solvers for their well-known computational efficiency. In this work, I benchmark a total of six solvers (two commercial and four open source) and measure their performance to solve linear and mixed-integer linear problems of increasing complexity. Although commercial solvers are still the fastest, at least two open-source solvers show comparable performance. These results show that genome-scale metabolic modeling does not need to be hindered by commercial licensing schemes and can become a truly open science framework for solving urgent societal challenges.IMPORTANCEModeling the metabolism of organisms and communities allows for computational exploration of their metabolic capabilities and testing their response to genetic and environmental perturbations. This holds the potential to address multiple societal issues related to human health and the environment. One of the current limitations is the use of commercial optimization solvers with restrictive licenses for academic and non-academic use. This work compares the performance of several commercial and open-source solvers to solve some of the most complex problems in the field. Benchmarking results show that, although commercial solvers are indeed faster, some of the open-source options can also efficiently tackle the hardest problems, showing great promise for the development of open science applications.
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Affiliation(s)
- Daniel Machado
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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15
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Gaballa A, Gebhardt-Wolf A, Krenz B, Mattavelli G, John M, Cossa G, Andreani S, Schülein-Völk C, Montesinos F, Vidal R, Kastner C, Ade CP, Kneitz B, Gasteiger G, Gallant P, Rosenfeldt M, Riedel A, Eilers M. PAF1c links S-phase progression to immune evasion and MYC function in pancreatic carcinoma. Nat Commun 2024; 15:1446. [PMID: 38365788 PMCID: PMC10873513 DOI: 10.1038/s41467-024-45760-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 02/05/2024] [Indexed: 02/18/2024] Open
Abstract
In pancreatic ductal adenocarcinoma (PDAC), endogenous MYC is required for S-phase progression and escape from immune surveillance. Here we show that MYC in PDAC cells is needed for the recruitment of the PAF1c transcription elongation complex to RNA polymerase and that depletion of CTR9, a PAF1c subunit, enables long-term survival of PDAC-bearing mice. PAF1c is largely dispensable for normal proliferation and regulation of MYC target genes. Instead, PAF1c limits DNA damage associated with S-phase progression by being essential for the expression of long genes involved in replication and DNA repair. Surprisingly, the survival benefit conferred by CTR9 depletion is not due to DNA damage, but to T-cell activation and restoration of immune surveillance. This is because CTR9 depletion releases RNA polymerase and elongation factors from the body of long genes and promotes the transcription of short genes, including MHC class I genes. The data argue that functionally distinct gene sets compete for elongation factors and directly link MYC-driven S-phase progression to tumor immune evasion.
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Affiliation(s)
- Abdallah Gaballa
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Anneli Gebhardt-Wolf
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Bastian Krenz
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
- Mildred Scheel Early Career Center, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Greta Mattavelli
- Mildred Scheel Early Career Center, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Mara John
- Mildred Scheel Early Career Center, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Giacomo Cossa
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Silvia Andreani
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Christina Schülein-Völk
- Core Unit High-Content Microscopy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Francisco Montesinos
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Raphael Vidal
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Carolin Kastner
- Mildred Scheel Early Career Center, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Carsten P Ade
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Burkhard Kneitz
- Department of Urology and Pediatric Urology, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Georg Gasteiger
- Würzburg Institute of Systems Immunology, Max Planck Research Group, Julius Maximilian University Würzburg, Versbacher Str. 9, 97078, Würzburg, Germany
| | - Peter Gallant
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Mathias Rosenfeldt
- Institute of Pathology, Julius Maximilian University Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Angela Riedel
- Mildred Scheel Early Career Center, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Germany
| | - Martin Eilers
- Department of Biochemistry and Molecular Biologyy, Theodor Boveri Institute, Biocenter, Julius Maximilian University Würzburg, Am Hubland, 97074, Würzburg, Germany.
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, Josef-Schneider-Str. 2, 97080, Würzburg, Germany.
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16
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Ciężki S, Odyjewska E, Bossowski A, Głowińska-Olszewska B. Not Only Metabolic Complications of Childhood Obesity. Nutrients 2024; 16:539. [PMID: 38398863 PMCID: PMC10892374 DOI: 10.3390/nu16040539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/11/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
The increasing incidence of obesity in the pediatric population requires attention to its serious complications. It turns out that in addition to typical, well-known metabolic complications, obesity as a systemic disease carries the risk of equally serious, although less obvious, non-metabolic complications, such as cardiovascular diseases, polycystic ovary syndrome, chronic kidney disease, asthma, thyroid dysfunction, immunologic and dermatologic conditions, and mental health problems. They can affect almost all systems of the young body and also leave their mark in adulthood. In addition, obesity also contributes to the exacerbation of existing childhood diseases. As a result, children suffering from obesity may have a reduced quality of life, both physically and mentally, and their life expectancy may be shortened. It also turns out that, in the case of obese pregnant girls, the complications of obesity may also affect their unborn children. Therefore, it is extremely important to take all necessary actions to prevent the growing epidemic of obesity in the pediatric population, as well as to treat existing complications of obesity and detect them at an early stage. In summary, physicians treating a child with a systemic disease such as obesity must adopt a holistic approach to treatment.
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Affiliation(s)
- Sebastian Ciężki
- Department of Pediatrics, Endocrinology, and Diabetology with Cardiology Division, Medical University of Bialystok, 15-274 Białystok, Poland
| | - Emilia Odyjewska
- Department of Pediatrics, Endocrinology, and Diabetology with Cardiology Division, Medical University of Bialystok, 15-274 Białystok, Poland
| | - Artur Bossowski
- Department of Pediatrics, Endocrinology, and Diabetology with Cardiology Division, Medical University of Bialystok, 15-274 Białystok, Poland
| | - Barbara Głowińska-Olszewska
- Department of Pediatrics, Endocrinology, and Diabetology with Cardiology Division, Medical University of Bialystok, 15-274 Białystok, Poland
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17
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Ramanthrikkovil Variyam A, Stolov M, Feng J, Amdursky N. Solid-State Molecular Protonics Devices of Solid-Supported Biological Membranes Reveal the Mechanism of Long-Range Lateral Proton Transport. ACS Nano 2024; 18:5101-5112. [PMID: 38314693 PMCID: PMC10867892 DOI: 10.1021/acsnano.3c11990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/07/2024]
Abstract
Lateral proton transport (PT) on the surface of biological membranes is a fundamental biochemical process in the bioenergetics of living cells, but a lack of available experimental techniques has resulted in a limited understanding of its mechanism. Here, we present a molecular protonics experimental approach to investigate lateral PT across membranes by measuring long-range (70 μm) lateral proton conduction via a few layers of lipid bilayers in a solid-state-like environment, i.e., without having bulk water surrounding the membrane. This configuration enables us to focus on lateral proton conduction across the surface of the membrane while decoupling it from bulk water. Hence, by controlling the relative humidity of the environment, we can directly explore the role of water in the lateral PT process. We show that proton conduction is dependent on the number of water molecules and their structure and on membrane composition, where we explore the role of the headgroup, the tail saturation, the membrane phase, and membrane fluidity. The measured PT as a function of temperature shows an inverse temperature dependency, which we explain by the desorption and adsorption of water molecules into the solid membrane platform. We explain our findings by discussing the role of percolating hydrogen bonding within the membrane structure in a Grotthuss-like mechanism.
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Affiliation(s)
| | - Mikhail Stolov
- Wolfson
Department of Chemical Engineering, Technion
− Israel Institute of Technology, Haifa 3200003, Israel
| | - Jiajun Feng
- Schulich
Faculty of Chemistry, Technion −
Israel Institute of Technology, Haifa 3200003, Israel
| | - Nadav Amdursky
- Schulich
Faculty of Chemistry, Technion −
Israel Institute of Technology, Haifa 3200003, Israel
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18
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19
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Yin Y, Yu H, Wang X, Hu Q, Liu Z, Luo D, Yang X. Cytoophidia: a conserved yet promising mode of enzyme regulation in nucleotide metabolism. Mol Biol Rep 2024; 51:245. [PMID: 38300325 DOI: 10.1007/s11033-024-09208-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024]
Abstract
Nucleotide biosynthesis encompasses both de novo and salvage synthesis pathways, each characterized by significant material and procedural distinctions. Despite these differences, cells with elevated nucleotide demands exhibit a preference for the more intricate de novo synthesis pathway, intricately linked to modes of enzyme regulation. In this study, we primarily scrutinize the biological importance of a conserved yet promising mode of enzyme regulation in nucleotide metabolism-cytoophidia. Cytoophidia, comprising cytidine triphosphate synthase or inosine monophosphate dehydrogenase, is explored across diverse biological models, including yeasts, Drosophila, mice, and human cancer cell lines. Additionally, we delineate potential biomedical applications of cytoophidia. As our understanding of cytoophidia deepens, the roles of enzyme compartmentalization and polymerization in various biochemical processes will unveil, promising profound impacts on both research and the treatment of metabolism-related diseases.
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Affiliation(s)
- Yue Yin
- School of Queen Mary, Jiangxi Medical College, Nanchang University, Jiangxi, China
| | - Huanhuan Yu
- First School of Clinical Medicine, Jiangxi Medical College, Nanchang University, Jiangxi, China
| | - Xinyi Wang
- Thyroid Surgery Center, West China Hospital of Sichuan University, Chengdu, China
| | - Qiaohao Hu
- The 1st Affiliated Hospital, Jiangxi Medical College, Nanchang University, Jiangxi, China
| | - Zhuoqi Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Jiangxi Medical College, Nanchang University, Jiangxi, China
| | - Daya Luo
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Jiangxi Medical College, Nanchang University, Jiangxi, China.
| | - Xiaohong Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Jiangxi Medical College, Nanchang University, Jiangxi, China.
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20
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Kumar S, Chakraborty S, Chakraborty N. Dehydration-responsive cytoskeleton proteome of rice reveals reprograming of key molecular pathways to mediate metabolic adaptation and cell survival. Plant Physiol Biochem 2024; 207:108359. [PMID: 38237420 DOI: 10.1016/j.plaphy.2024.108359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/22/2023] [Accepted: 01/10/2024] [Indexed: 03/16/2024]
Abstract
The plant cytoskeletal proteins play a key role that control cytoskeleton dynamics, contributing to crucial biological processes such as cell wall morphogenesis, stomatal conductance and abscisic acid accumulation in repercussion to water-deficit stress or dehydration. Yet, it is still completely unknown which specific biochemical processes and regulatory mechanisms the cytoskeleton uses to drive dehydration tolerance. To better understand the role of cytoskeleton, we developed the dehydration-responsive cytoskeletal proteome map of a resilient rice cultivar. Initially, four-week-old rice plants were exposed to progressive dehydration, and the magnitude of dehydration-induced compensatory physiological responses was monitored in terms of physicochemical indices. The organelle fractionation in conjunction with label-free quantitative proteome analysis led to the identification of 955 dehydration-responsive cytoskeletal proteins (DRCPs). To our knowledge, this is the first report of a stress-responsive plant cytoskeletal proteome, representing the largest inventory of cytoskeleton and cytoskeleton-associated proteins. The DRCPs were apparently involved in a wide array of intra-cellular molecules transportation, organelles positioning, cytoskeleton organization followed by different metabolic processes including amino acid metabolism. These findings presented open a unique view on global regulation of plant cytoskeletal proteome is intimately linked to cellular metabolic rewiring of adaptive responses, and potentially confer dehydration tolerance, especially in rice, and other crop species, in general.
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Affiliation(s)
- Sunil Kumar
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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21
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Burke KA, Urick CD, Mzhavia N, Nikolich MP, Filippov AA. Correlation of Pseudomonas aeruginosa Phage Resistance with the Numbers and Types of Antiphage Systems. Int J Mol Sci 2024; 25:1424. [PMID: 38338703 PMCID: PMC10855318 DOI: 10.3390/ijms25031424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Phage therapeutics offer a potentially powerful approach for combating multidrug-resistant bacterial infections. However, to be effective, phage therapy must overcome existing and developing phage resistance. While phage cocktails can reduce this risk by targeting multiple receptors in a single therapeutic, bacteria have mechanisms of resistance beyond receptor modification. A rapidly growing body of knowledge describes a broad and varied arsenal of antiphage systems encoded by bacteria to counter phage infection. We sought to understand the types and frequencies of antiphage systems present in a highly diverse panel of Pseudomonas aeruginosa clinical isolates utilized to characterize novel antibacterials. Using the web-server tool PADLOC (prokaryotic antiviral defense locator), putative antiphage systems were identified in these P. aeruginosa clinical isolates based on sequence homology to a validated and curated catalog of known defense systems. Coupling this host bacterium sequence analysis with host range data for 70 phages, we observed a correlation between existing phage resistance and the presence of higher numbers of antiphage systems in bacterial genomes. We were also able to identify antiphage systems that were more prevalent in highly phage-resistant P. aeruginosa strains, suggesting their importance in conferring resistance.
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Affiliation(s)
| | | | | | | | - Andrey A. Filippov
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (K.A.B.); (C.D.U.); (N.M.); (M.P.N.)
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22
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Fell DA, Saavedra E, Rohwer J. 50 years of Metabolic Control Analysis: Its past and current influence in the biological sciences. Biosystems 2024; 235:105086. [PMID: 37979831 DOI: 10.1016/j.biosystems.2023.105086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2023]
Affiliation(s)
- David A Fell
- Dept. of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK.
| | - Emma Saavedra
- Department of Biochemistry, Instituto Nacional de Cardiologia Ignacio Chavez, Mexico City, Mexico.
| | - Johann Rohwer
- Department of Biochemistry, Stellenbosch University, Stellenbosch, 7600, South Africa.
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23
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Gorsheneva NA, Sopova JV, Azarov VV, Grizel AV, Rubel AA. Biomolecular Condensates: Structure, Functions, Methods of Research. Biochemistry (Mosc) 2024; 89:S205-S223. [PMID: 38621751 DOI: 10.1134/s0006297924140116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 04/17/2024]
Abstract
The term "biomolecular condensates" is used to describe membraneless compartments in eukaryotic cells, accumulating proteins and nucleic acids. Biomolecular condensates are formed as a result of liquid-liquid phase separation (LLPS). Often, they demonstrate properties of liquid-like droplets or gel-like aggregates; however, some of them may appear to have a more complex structure and high-order organization. Membraneless microcompartments are involved in diverse processes both in cytoplasm and in nucleus, among them ribosome biogenesis, regulation of gene expression, cell signaling, and stress response. Condensates properties and structure could be highly dynamic and are affected by various internal and external factors, e.g., concentration and interactions of components, solution temperature, pH, osmolarity, etc. In this review, we discuss variety of biomolecular condensates and their functions in live cells, describe their structure variants, highlight domain and primary sequence organization of the constituent proteins and nucleic acids. Finally, we describe current advances in methods that characterize structure, properties, morphology, and dynamics of biomolecular condensates in vitro and in vivo.
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Affiliation(s)
| | - Julia V Sopova
- St. Petersburg State University, St. Petersburg, 199034, Russia.
| | | | - Anastasia V Grizel
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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24
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Nutrient uptake strategies shift during mouse epiblast development. Nat Metab 2024; 6:16-7. [PMID: 38172383 DOI: 10.1038/s42255-023-00941-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
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25
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Kobercová E, Melo P, Fischer L. Validating the role of glutamine synthetase GLN2 during photorespiration in Arabidopsis thaliana. Plant Physiol 2023; 194:324-328. [PMID: 37787606 PMCID: PMC10756748 DOI: 10.1093/plphys/kiad521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/04/2023]
Affiliation(s)
- Eliška Kobercová
- Faculty of Science, Department of Experimental Plant Biology, Charles University, Viničná 5, Prague 2, 128 44, Czech Republic
| | - Paula Melo
- Faculty of Sciences, Department of Biology and GreenUPorto - Research Centre on Sustainable Agrifood Production, University of Porto, Rua do Campo Alegre s/n, Porto, 4169-007, Portugal
| | - Lukáš Fischer
- Faculty of Science, Department of Experimental Plant Biology, Charles University, Viničná 5, Prague 2, 128 44, Czech Republic
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26
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Hong Y, Qin J, Totsika M. A conditional nature for the synthetical lethality between defects in lipid and peptidoglycan biosynthesis. Proc Natl Acad Sci U S A 2023; 120:e2318882120. [PMID: 38109534 PMCID: PMC10756204 DOI: 10.1073/pnas.2318882120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023] Open
Affiliation(s)
- Yaoqin Hong
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, QLD4006, Australia
- Max Planck Queensland Centre, Queensland University of Technology, QLD4006, Australia
| | - Jilong Qin
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, QLD4006, Australia
| | - Makrina Totsika
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, QLD4006, Australia
- Max Planck Queensland Centre, Queensland University of Technology, QLD4006, Australia
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27
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Zhilyaeva TV, Kasyanov ED, Rukavishnikov GV, Piatoikina AS, Bavrina AP, Kostina OV, Zhukova ES, Shcherbatyuk TG, Mazo GE. Pterin metabolism, inflammation and oxidative stress biochemical markers in schizophrenia: Factor analysis and assessment of clinical symptoms associations. Prog Neuropsychopharmacol Biol Psychiatry 2023; 127:110823. [PMID: 37437837 DOI: 10.1016/j.pnpbp.2023.110823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/30/2023] [Accepted: 07/07/2023] [Indexed: 07/14/2023]
Abstract
Various aspects of folate and tetrahydrobiopterin (BH4) metabolism disturbances have been detected in patients with schizophrenia.Data were obtained that disturbances in the pterins (folates and BH4) metabolism can be associated with oxidative stress and inflammation, but has not yet been confirmed in clinical studies in schizophrenia. Within the framework of this study, a correlation and factor analysis of biochemical markersof pterin metabolism, inflammation and redox imbalance in patients with schizophrenia was performed in order to test the hypothesis of the single etiopathogenetic node, including the studied biochemical processes. Methods: 125 patients with schizophrenia and 95 healthy volunteers were randomly selected and evaluated with a biochemical examination of BH4, folate, B12, homocysteine, C-reactive protein, interleukin-6, reduced glutathione levels in the blood serum; activity of superoxide dismutase and catalase - in erythrocytes; malondialdehyde - in blood plasma. All patients underwent an examination using standardized psychopathology rating scales. Spearman rank coefficient (ρ) with Benjamini-Hochberg correction was used for the correlation analysis. The principal components analysis (PCA) was used as a factor analysis. Results: Significant correlations were found within groups of pterin metabolism, inflammatory markers and redox-imbalance, and also between separate inflammation, oxidative stress and markers of pterin metabolism. The performed factor analysis made it possible to distinguish two components: 1 - pterin metabolism, 2 - oxidativeinflammatory markers. Despite the weak statistical associations and, possibly, functional relationships between pterin metabolism and oxidative/inflammation markers, each of the components has its own clinical correlates and, probably, a separate contribution to the pathology of schizophrenia.
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Affiliation(s)
- T V Zhilyaeva
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia; V.M. Bekhterev National Medical Research Center for Psychiatry and Neurology, St. Petersburg, Russia.
| | - E D Kasyanov
- V.M. Bekhterev National Medical Research Center for Psychiatry and Neurology, St. Petersburg, Russia
| | - G V Rukavishnikov
- V.M. Bekhterev National Medical Research Center for Psychiatry and Neurology, St. Petersburg, Russia
| | - A S Piatoikina
- Nizhny Novgorod Clinical Psychiatric, Hospital No. 1, Nizhny Novgorod, Russia
| | - A P Bavrina
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - O V Kostina
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - E S Zhukova
- Nizhny Novgorod Research Institute for Hygiene and Occupational Pathology, Nizhny Novgorod, Russia
| | - T G Shcherbatyuk
- Nizhny Novgorod Research Institute for Hygiene and Occupational Pathology, Nizhny Novgorod, Russia; Pushchino State Institute of Natural Science, Pushchino, Russia
| | - G E Mazo
- V.M. Bekhterev National Medical Research Center for Psychiatry and Neurology, St. Petersburg, Russia
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28
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Nie X, Deng Y, Tong X, Han F. Editorial: Mechanism and therapeutic potential of macrophages in metabolic and cardiovascular diseases. Front Immunol 2023; 14:1352567. [PMID: 38173724 PMCID: PMC10763238 DOI: 10.3389/fimmu.2023.1352567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Affiliation(s)
- Xuqiang Nie
- College of Pharmacy, Zunyi Medical University, Guizhou, China
- Joint International Research Laboratory of Ethnomedicine of Ministry of Education & Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Guizhou, China
| | - Youcai Deng
- Department of Clinical Hematology, College of Pharmacy and Laboratory Medicine Science, Army Medical University, Chongqing, China
| | - Xiaoyong Tong
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Felicity Han
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
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29
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Walters H. Mechanical resistance to tumor initiation deteriorates with tissue aging. Nat Aging 2023; 3:1469. [PMID: 38052931 DOI: 10.1038/s43587-023-00545-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
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30
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Lim R, Martin TLP, Chae J, Kim WJ, Ghim CM, Kim PJ. Generalized Michaelis-Menten rate law with time-varying molecular concentrations. PLoS Comput Biol 2023; 19:e1011711. [PMID: 38079453 PMCID: PMC10735182 DOI: 10.1371/journal.pcbi.1011711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 12/21/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
The Michaelis-Menten (MM) rate law has been the dominant paradigm of modeling biochemical rate processes for over a century with applications in biochemistry, biophysics, cell biology, systems biology, and chemical engineering. The MM rate law and its remedied form stand on the assumption that the concentration of the complex of interacting molecules, at each moment, approaches an equilibrium (quasi-steady state) much faster than the molecular concentrations change. Yet, this assumption is not always justified. Here, we relax this quasi-steady state requirement and propose the generalized MM rate law for the interactions of molecules with active concentration changes over time. Our approach for time-varying molecular concentrations, termed the effective time-delay scheme (ETS), is based on rigorously estimated time-delay effects in molecular complex formation. With particularly marked improvements in protein-protein and protein-DNA interaction modeling, the ETS provides an analytical framework to interpret and predict rich transient or rhythmic dynamics (such as autogenously-regulated cellular adaptation and circadian protein turnover), which goes beyond the quasi-steady state assumption.
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Affiliation(s)
- Roktaek Lim
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | | | - Junghun Chae
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Woo Joong Kim
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Cheol-Min Ghim
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Pan-Jun Kim
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong
- Center for Quantitative Systems Biology & Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Kowloon, Hong Kong
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon, Hong Kong
- Abdus Salam International Centre for Theoretical Physics, Trieste, Italy
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31
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Cheah JS. Unbiased mapping of protein trafficking with TransitID. Nat Rev Mol Cell Biol 2023; 24:853. [PMID: 37604995 DOI: 10.1038/s41580-023-00653-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Affiliation(s)
- Joleen S Cheah
- Department of Biology, Stanford University, Stanford, CA, USA.
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32
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Bremmer F. [Teratoma with somatic-type malignancy : Analyses to characterize the mutations, DNA methylation, and proteome]. Pathologie (Heidelb) 2023; 44:109-112. [PMID: 38047949 DOI: 10.1007/s00292-023-01282-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/30/2023] [Indexed: 12/05/2023]
Affiliation(s)
- F Bremmer
- Institut für Pathologie, Universitätsmedizin Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Deutschland.
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Tian Y, Wan N, Zhang H, Shao C, Ding M, Bao Q, Hu H, Sun H, Liu C, Zhou K, Chen S, Wang G, Ye H, Hao H. Chemoproteomic mapping of the glycolytic targetome in cancer cells. Nat Chem Biol 2023; 19:1480-1491. [PMID: 37322158 DOI: 10.1038/s41589-023-01355-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Abstract
Hyperactivated glycolysis is a metabolic hallmark of most cancer cells. Although sporadic information has revealed that glycolytic metabolites possess nonmetabolic functions as signaling molecules, how these metabolites interact with and functionally regulate their binding targets remains largely elusive. Here, we introduce a target-responsive accessibility profiling (TRAP) approach that measures changes in ligand binding-induced accessibility for target identification by globally labeling reactive proteinaceous lysines. With TRAP, we mapped 913 responsive target candidates and 2,487 interactions for 10 major glycolytic metabolites in a model cancer cell line. The wide targetome depicted by TRAP unveils diverse regulatory modalities of glycolytic metabolites, and these modalities involve direct perturbation of enzymes in carbohydrate metabolism, intervention of an orphan transcriptional protein's activity and modulation of targetome-level acetylation. These results further our knowledge of how glycolysis orchestrates signaling pathways in cancer cells to support their survival, and inspire exploitation of the glycolytic targetome for cancer therapy.
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Affiliation(s)
- Yang Tian
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Ning Wan
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Hanqing Zhang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Chang Shao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Ming Ding
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Qiuyu Bao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Haiyang Hu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Huiyong Sun
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Chenguang Liu
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Kun Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Shuai Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Guangji Wang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Hui Ye
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
| | - Haiping Hao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
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Lopes KG, Rodrigues EL, da Silva Lopes MR, do Nascimento VA, Pott A, Guimarães RDCA, Pegolo GE, Freitas KDC. Reply to Boucher, B.J. Comment on "Lopes et al. Adiposity Metabolic Consequences for Adolescent Bone Health. Nutrients 2022, 14, 3260". Nutrients 2023; 15:4953. [PMID: 38068812 PMCID: PMC10708121 DOI: 10.3390/nu15234953] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
We appreciate your careful reading and comments [...].
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Affiliation(s)
- Kátia Gianlupi Lopes
- Post-Graduate Program in Health and Development in the Mid-West Region, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil; (K.G.L.); (E.L.R.); (M.R.d.S.L.); (V.A.d.N.); (R.d.C.A.G.)
| | - Elisana Lima Rodrigues
- Post-Graduate Program in Health and Development in the Mid-West Region, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil; (K.G.L.); (E.L.R.); (M.R.d.S.L.); (V.A.d.N.); (R.d.C.A.G.)
| | - Mariana Rodrigues da Silva Lopes
- Post-Graduate Program in Health and Development in the Mid-West Region, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil; (K.G.L.); (E.L.R.); (M.R.d.S.L.); (V.A.d.N.); (R.d.C.A.G.)
| | - Valter Aragão do Nascimento
- Post-Graduate Program in Health and Development in the Mid-West Region, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil; (K.G.L.); (E.L.R.); (M.R.d.S.L.); (V.A.d.N.); (R.d.C.A.G.)
| | - Arnildo Pott
- Institute of Biosciences, Federal University of Mato Grosso do Sul-UFMS, Campo Grande 79079-900, Brazil;
| | - Rita de Cássia Avellaneda Guimarães
- Post-Graduate Program in Health and Development in the Mid-West Region, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil; (K.G.L.); (E.L.R.); (M.R.d.S.L.); (V.A.d.N.); (R.d.C.A.G.)
| | - Giovana Eliza Pegolo
- Faculty of Pharmaceutical Sciences, Food and Nutrition, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil;
| | - Karine de Cássia Freitas
- Post-Graduate Program in Health and Development in the Mid-West Region, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil; (K.G.L.); (E.L.R.); (M.R.d.S.L.); (V.A.d.N.); (R.d.C.A.G.)
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Liu M, Ji M, Cheng J, Li Y, Tian Y, Zhao H, Wang Y, Zhu S, Zhang L, Xu X, Feng GS, Liang X, Bao H, Tang Y, Kong S, Lu J, Wang H, Lu Z, Deng W. Deciphering a critical role of uterine epithelial SHP2 in parturition initiation at single cell resolution. Nat Commun 2023; 14:7356. [PMID: 37963860 PMCID: PMC10646072 DOI: 10.1038/s41467-023-43102-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 10/31/2023] [Indexed: 11/16/2023] Open
Abstract
The timely onset of female parturition is a critical determinant for pregnancy success. The highly heterogenous maternal decidua has been increasingly recognized as a vital factor in setting the timing of labor. Despite the cell type specific roles in parturition, the role of the uterine epithelium in the decidua remains poorly understood. This study uncovers the critical role of epithelial SHP2 in parturition initiation via COX1 and COX2 derived PGF2α leveraging epithelial specific Shp2 knockout mice, whose disruption contributes to delayed parturition initiation, dystocia and fetal deaths. Additionally, we also show that there are distinct types of epithelium in the decidua approaching parturition at single cell resolution accompanied with profound epithelium reformation via proliferation. Meanwhile, the epithelium maintains the microenvironment by communicating with stromal cells and macrophages. The epithelial microenvironment is maintained by a close interaction among epithelial, stromal and macrophage cells of uterine stromal cells. In brief, this study provides a previously unappreciated role of the epithelium in parturition preparation and sheds lights on the prevention of preterm birth.
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Affiliation(s)
- Meng Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, China
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Mengjun Ji
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jianghong Cheng
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yingzhe Li
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yingpu Tian
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Hui Zhao
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Yang Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Sijing Zhu
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Leilei Zhang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Xinmei Xu
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Gen-Sheng Feng
- Department of Pathology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Xiaohuan Liang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Haili Bao
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Yedong Tang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Shuangbo Kong
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Jinhua Lu
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Haibin Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China.
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Medicine, Xiamen University, Xiamen, Fujian, China.
| | - Zhongxian Lu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, China.
| | - Wenbo Deng
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361102, China.
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Medicine, Xiamen University, Xiamen, Fujian, China.
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Kurter H, Basbinar Y, Ellidokuz H, Calibasi-Kocal G. The Role of Cyanidin-3- O-glucoside in Modulating Oxaliplatin Resistance by Reversing Mesenchymal Phenotype in Colorectal Cancer. Nutrients 2023; 15:4705. [PMID: 38004099 PMCID: PMC10674439 DOI: 10.3390/nu15224705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Epithelial-mesenchymal transition (EMT) plays an important role in the biological and biochemical processes of cells, and it is a critical process in the malignant transformation, and mobility of cancer. Additionally, EMT is one of the main mechanisms contributing to chemoresistance. Resistance to oxaliplatin (OXA) poses a momentous challenge in the chemotherapy of advanced colorectal cancer (CRC) patients, highlighting the need to reverse drug resistance and improve patient survival. In this study, we explored the response of cyanidin-3-O-glucoside (C3G), the most abundant anthocyanin in plants, on the mechanisms of drug resistance in cancer, with the purpose of overcoming acquired OXA resistance in CRC cell lines. METHODS We generated an acquired OXA-resistant cell line, named HCT-116-ROx, by gradually exposing parental HCT-116 cells to increasing concentrations of OXA. To characterize the resistance, we performed cytotoxicity assays and shape factor analyses. The apoptotic rate of both resistant and parental cells was determined using Hoechst 33342/Propidium Iodide (PI) fluorescence staining. Migration capacity was evaluated using a wound-healing assay. The mesenchymal phenotype was assessed through qRT-PCR and immunofluorescence staining, employing E-cadherin, N-cadherin, and Vimentin markers. RESULTS Resistance characterization announced decreased OXA sensitivity in resistant cells compared to parental cells. Moreover, the resistant cells exhibited a spindle cell morphology, indicative of the mesenchymal phenotype. Combined treatment of C3G and OXA resulted in an augmented apoptotic rate in the resistant cells. The migration capacity of resistant cells was higher than parental cells, while treatment with C3G decreased the migration rate of HCT-116-ROx cells. Analysis of EMT markers showed that HCT-116-ROx cells exhibited loss of the epithelial phenotype (E-cadherin) and gain of the mesenchymal phenotype (N-cadherin and Vimentin) compared to HCT-116 cells. However, treatment of resistant cells with C3G reversed the mesenchymal phenotype. CONCLUSION The morphological observations of cells acquiring oxaliplatin resistance indicated the loss of the epithelial phenotype and the acquisition of the mesenchymal phenotype. These findings suggest that EMT may contribute to acquired OXA resistance in CRC. Furthermore, C3G decreased the mobility of resistant cells, and reversed the EMT process, indicating its potential to overcome acquired OXA resistance.
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Affiliation(s)
- Hasan Kurter
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir 35330, Turkey;
| | - Yasemin Basbinar
- Department of Translational Oncology, Institute of Oncology, Dokuz Eylul University, Izmir 35330, Turkey;
| | - Hulya Ellidokuz
- Department of Preventive Oncology, Institute of Oncology, Dokuz Eylul University, Izmir 35330, Turkey;
| | - Gizem Calibasi-Kocal
- Department of Translational Oncology, Institute of Oncology, Dokuz Eylul University, Izmir 35330, Turkey;
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37
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Pokojná H, Kozlíková B, Berry D, Kriglstein S, Furmanová K. Seeing the unseen: Comparison study of representation approaches for biochemical processes in education. PLoS One 2023; 18:e0293592. [PMID: 37930950 PMCID: PMC10627439 DOI: 10.1371/journal.pone.0293592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 10/06/2023] [Indexed: 11/08/2023] Open
Abstract
The representations of biochemical processes must balance visual portrayals with descriptive content to be an effective learning tool. To determine what type of representation is the most suitable for education, we designed five different representations of adenosine triphosphate (ATP) synthesis and examined how they are perceived. Our representations consisted of an overview of the process in a detailed and abstract illustrative format, continuous video formats with and without narration, and a combined illustrative overview with dynamic components. The five representations were evaluated by non-experts who were randomly assigned one of them and experts who viewed and compared all five representations. Subsequently, we conducted a focus group on the outcomes of these evaluations, which gave insight into possible explanations of our results, where the non-experts preferred the detailed static representation and found the narrated video least helpful, in contradiction to the experts who favored the narrated video the most.
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Affiliation(s)
- Hana Pokojná
- Department of Visual Computing, Masaryk University, Brno, Czech Republic
| | - Barbora Kozlíková
- Department of Visual Computing, Masaryk University, Brno, Czech Republic
| | - Drew Berry
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Simone Kriglstein
- Department of Visual Computing, Masaryk University, Brno, Czech Republic
- AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Katarína Furmanová
- Department of Visual Computing, Masaryk University, Brno, Czech Republic
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Ghosheh M, Ehrlich A, Ioannidis K, Ayyash M, Goldfracht I, Cohen M, Fischer A, Mintz Y, Gepstein L, Nahmias Y. Electro-metabolic coupling in multi-chambered vascularized human cardiac organoids. Nat Biomed Eng 2023; 7:1493-1513. [PMID: 37550423 DOI: 10.1038/s41551-023-01071-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 06/27/2023] [Indexed: 08/09/2023]
Abstract
The study of cardiac physiology is hindered by physiological differences between humans and small-animal models. Here we report the generation of multi-chambered self-paced vascularized human cardiac organoids formed under anisotropic stress and their applicability to the study of cardiac arrhythmia. Sensors embedded in the cardiac organoids enabled the simultaneous measurement of oxygen uptake, extracellular field potentials and cardiac contraction at resolutions higher than 10 Hz. This microphysiological system revealed 1 Hz cardiac respiratory cycles that are coupled to the electrical rather than the mechanical activity of cardiomyocytes. This electro-mitochondrial coupling was driven by mitochondrial calcium oscillations driving respiration cycles. Pharmaceutical or genetic inhibition of this coupling results in arrhythmogenic behaviour. We show that the chemotherapeutic mitoxantrone induces arrhythmia through disruption of this pathway, a process that can be partially reversed by the co-administration of metformin. Our microphysiological cardiac systems may further facilitate the study of the mitochondrial dynamics of cardiac rhythms and advance our understanding of human cardiac physiology.
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Affiliation(s)
- Mohammad Ghosheh
- Alexander Grass Center for Bioengineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avner Ehrlich
- Alexander Grass Center for Bioengineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Tissue Dynamics, LTD, Jerusalem, Israel
| | - Konstantinos Ioannidis
- Alexander Grass Center for Bioengineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Tissue Dynamics, LTD, Jerusalem, Israel
| | - Muneef Ayyash
- Alexander Grass Center for Bioengineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Idit Goldfracht
- Sohnis Research Laboratory for Cardiac Electrophysiology and Regenerative Medicine, the Rappaport Faculty of Medicine and Research Institute, Technion- Israel Institute of Technology, Haifa, Israel
| | - Merav Cohen
- Alexander Grass Center for Bioengineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Cell and Developmental Biology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amit Fischer
- Department of Biological Chemistry, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yoav Mintz
- Department of General Surgery, Hadassah Hebrew University Medical Center, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lior Gepstein
- Sohnis Research Laboratory for Cardiac Electrophysiology and Regenerative Medicine, the Rappaport Faculty of Medicine and Research Institute, Technion- Israel Institute of Technology, Haifa, Israel
- Cardiology Department, Rambam Health Care Campus, Haifa, Israel
| | - Yaakov Nahmias
- Alexander Grass Center for Bioengineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Tissue Dynamics, LTD, Jerusalem, Israel.
- Department of Cell and Developmental Biology, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Yi X, Chang ML, Zhou ZD, Yi L, Yuan H, Qi J, Yi L, Huan JN, Huang XQ. LPS induces SGPP2 to participate metabolic reprogramming in endothelial cells. Free Radic Biol Med 2023; 208:780-793. [PMID: 37703934 DOI: 10.1016/j.freeradbiomed.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 08/12/2023] [Accepted: 09/08/2023] [Indexed: 09/15/2023]
Abstract
Sepsis often causes organ dysfunction and is manifested in increased endothelial cell permeability in blood vessels. Early-stage inflammation is accompanied by metabolic changes, but it is unclear how the metabolic alterations in the endothelial cells following lipopolysaccharide (LPS) stimulation affect endothelial cell function. In this study, the effects of 1 μg/ml of LPS on the metabolism of human umbilical vein endothelial cells (HUVECs) were investigated, and the metabolic changes after LPS stimulation were explained from the perspective of mRNA expression, chromatin openness and metabolic flux. We found changes in the central metabolism of endothelial cells after LPS stimulation, such as enhanced glycolysis function, decreased mitochondrial membrane potential, and increased production of reactive oxygen species (ROS). Sphingolipid metabolic pathways change at the transcriptome level, and sphingosine-1-phosphatase 2 (SGPP2) was upregulated in LPS-stimulated endothelial cells and zebrafish models. Overexpression of SGPP2 improved cell barrier function, enhanced mitochondrial respiration capacity, but also produced oxidative respiration chain uncoupling. In addition, SGPP2 overexpression inhibited the degradation of HIF-1α protein. The molecular and biochemical processes identified in this study are not only beneficial for understanding the metabolic-related mechanisms of LPS-induced endothelial injury, but also for the discovery of general therapeutic targets for inflammation and inflammation-related diseases.
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Affiliation(s)
- Xin Yi
- Department of Burn, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meng-Ling Chang
- Department of Burn, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zeng-Ding Zhou
- Department of Burn, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Yi
- Department of Burn, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Yuan
- Shanghai Institute of Hematology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jin Qi
- Department of Orthopedics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Yi
- Department of Burn, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jing-Ning Huan
- Department of Burn, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xiao-Qin Huang
- Department of Burn, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Fischer T, Köhler L, Engel PD, Song C, Gärtner W, Wachtveitl J, Slavov C. Conserved tyrosine in phytochromes controls the photodynamics through steric demand and hydrogen bonding capabilities. Biochim Biophys Acta Bioenerg 2023; 1864:148996. [PMID: 37437858 DOI: 10.1016/j.bbabio.2023.148996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/02/2023] [Accepted: 07/06/2023] [Indexed: 07/14/2023]
Abstract
Using ultrafast spectroscopy and site-specific mutagenesis, we demonstrate the central role of a conserved tyrosine within the chromophore binding pocket in the forward (Pr → Pfr) photoconversion of phytochromes. Taking GAF1 of the knotless phytochrome All2699g1 from Nostoc as representative member of phytochromes, it was found that the mutations have no influence on the early (<30 ps) dynamics associated with conformational changes of the chromophore in the excited state. Conversely, they drastically impact the extended protein-controlled excited state decay (>100 ps). Thus, the steric demand, position and H-bonding capabilities of the identified tyrosine control the chromophore photoisomerization while leaving the excited state chromophore dynamics unaffected. In effect, this residue operates as an isomerization-steric-gate that tunes the excited state lifetime and the photoreaction efficiency by modulating the available space of the chromophore and by stabilizing the primary intermediate Lumi-R. Understanding the role of such a conserved structural element sheds light on a key aspect of phytochrome functionality and provides a basis for rational design of optimized photoreceptors for biotechnological applications.
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Affiliation(s)
- Tobias Fischer
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt, Germany.
| | - Lisa Köhler
- Institute for Analytical Chemistry, University of Leipzig, Linnéstraße 3, 04103 Leipzig, Germany.
| | - Philipp D Engel
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt, Germany.
| | - Chen Song
- Institute for Analytical Chemistry, University of Leipzig, Linnéstraße 3, 04103 Leipzig, Germany.
| | - Wolfgang Gärtner
- Institute for Analytical Chemistry, University of Leipzig, Linnéstraße 3, 04103 Leipzig, Germany.
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt, Germany.
| | - Chavdar Slavov
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt, Germany; Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, 33620 Tampa, United States of America.
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Oh CK, Piña-Crespo J, Talantova M, Carnevale LN, Stoneham C, Lewinski M, Guatelli J, Lipton SA. Reply to: Targeted protein S-nitrosylation of ACE2 inhibits SARS-CoV-2 infection. Nat Chem Biol 2023; 19:1306-1308. [PMID: 37798355 DOI: 10.1038/s41589-023-01425-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 08/22/2023] [Indexed: 10/07/2023]
Affiliation(s)
- Chang-Ki Oh
- Departments of Molecular Medicine and Neuroscience, Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Juan Piña-Crespo
- Departments of Molecular Medicine and Neuroscience, Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Maria Talantova
- Departments of Molecular Medicine and Neuroscience, Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Lauren N Carnevale
- Departments of Molecular Medicine and Neuroscience, Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Charlotte Stoneham
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- VA San Diego Healthcare System, San Diego, CA, USA
| | - Mary Lewinski
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- VA San Diego Healthcare System, San Diego, CA, USA
| | - John Guatelli
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- VA San Diego Healthcare System, San Diego, CA, USA
| | - Stuart A Lipton
- Departments of Molecular Medicine and Neuroscience, Neurodegeneration New Medicines Center, The Scripps Research Institute, La Jolla, CA, USA.
- Department of Neurosciences, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
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Jiang M, Yin J, Zhixue C, Munang’andu HM. Editorial: Metabolic regulation in immune processes against microbial infections. Front Immunol 2023; 14:1320443. [PMID: 37965308 PMCID: PMC10641868 DOI: 10.3389/fimmu.2023.1320443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 10/19/2023] [Indexed: 11/16/2023] Open
Affiliation(s)
- Ming Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jie Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Cheng Zhixue
- Department of Pulmonary and Critical Care Medicine Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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Sanclemente MA. Got vitamin C? A metabolic GWAS analysis identified a PAS/LOV PROTEIN regulating ascorbate accumulation. Plant Physiology 2023; 193:1721-1723. [PMID: 37619979 DOI: 10.1093/plphys/kiad462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/26/2023]
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Potęga A, Göldner V, Niehaves E, Paluszkiewicz E, Karst U. Electrochemistry/mass spectrometry (EC/MS) for fast generation and identification of novel reactive metabolites of two unsymmetrical bisacridines with anticancer activity. J Pharm Biomed Anal 2023; 235:115607. [PMID: 37523868 DOI: 10.1016/j.jpba.2023.115607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/28/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023]
Abstract
The development of a new drug requires knowledge about its metabolic fate in a living organism, regarding the comprehensive assessment of both drug therapeutic activity and toxicity profiles. Electrochemistry (EC) coupled with mass spectrometry (MS) is an efficient tool for predicting the phase I metabolism of redox-sensitive drugs. In particular, EC/MS represents a clear advantage for the generation of reactive drug transformation products and their direct identification compared to biological matrices. In this work, we focused on the characterization of novel electrochemical products of two representative unsymmetrical bisacridines (C-2028 and C-2045) with demonstrated high anticancer activity. The electrochemical thin-layer flow-through cell μ-PrepCell 2.0 (Antec Scientific) was used here for the effective metabolite electrosynthesis. The electrochemical simulation of C-2028 reductive and C-2045 oxidative metabolism resulted in the generation of new products that were not observed before. The formation of nitroso [M-O+H]+ and azoxy [2M-3O+H]+ species from C-2028, as well as a series of hydroxylated and/or dehydrogenated products, including possible quinones [M-2H+H]+ and [M+O-2H+H]+ from C-2045, was demonstrated. For the latter, a glutathione S-conjugate (m/z 935.3130) was also obtained in measurements supplemented with the excess of reduced glutathione. For the identification of the products of interest, structural confirmation based on MS/MS fragmentation experiments was performed. Novel products of electrochemical conversions of unsymmetrical bisacridines were discussed in the context of their possible biological effect on the human organism.
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Affiliation(s)
- Agnieszka Potęga
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry and BioTechMed Center, Gdańsk University of Technology, Gabriela Narutowicza Street 11/12, 80-233 Gdańsk, Poland.
| | - Valentin Göldner
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, 48149 Münster, Germany; International Graduate School for Battery Chemistry, Characterization, Analysis, Recycling and Application (BACCARA), University of Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Erik Niehaves
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Ewa Paluszkiewicz
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry and BioTechMed Center, Gdańsk University of Technology, Gabriela Narutowicza Street 11/12, 80-233 Gdańsk, Poland
| | - Uwe Karst
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 48, 48149 Münster, Germany; International Graduate School for Battery Chemistry, Characterization, Analysis, Recycling and Application (BACCARA), University of Münster, Corrensstraße 40, 48149 Münster, Germany
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McFadden T, Carucci I, Farrell K, Fletchall E, Jarome TJ. Hypothalamic DNA 5-hydroxymethylation levels are altered by diet-induced weight gain during the development of obesity in a sex-specific manner. Brain Res 2023; 1817:148478. [PMID: 37422205 PMCID: PMC10529936 DOI: 10.1016/j.brainres.2023.148478] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 07/10/2023]
Abstract
Obesity is a major health concern that is associated with altered gene transcription in the hypothalamus. However, the mechanisms controlling this gene expression dysregulation remain largely unknown. DNA 5-hydroxymethylation (5-hmC) is a potent transcriptional activator that is expressed at 10 times higher levels in the brain than the periphery. Despite this, no study has examined if DNA 5-hmC is altered in the brain following exposure to obesogenic diets or contributes to abnormal weight gain over time. Here, we used a rodent diet-induced obesity model in combination with quantitative molecular assays and CRISPR-dCas9 manipulations to test the role of hypothalamic DNA 5-hmC in abnormal weight gain in male and female rats. We found that males, but not females, have decreased levels of DNA 5-hmC in the hypothalamus following exposure to a high fat diet, which directly correlate with increased body weight. Short-term exposure to a high fat diet, which does not result in significant weight gain, resulted in decreased hypothalamic DNA 5-hmC levels, suggesting these changes occur prior to obesity development. Moreover, decreases in DNA 5-hmC persist even after the high fat diet is removed, though the extent of this is diet-dependent. Importantly, CRISPR-dCas9-mediated upregulation of DNA 5-hmC enzymes in the male, but not female, ventromedial nucleus of the hypothalamus significantly reduced the percentage of weight gained on the high fat diet relative to controls. These results suggest that hypothalamic DNA 5-hmC is an important sex-specific regulator of abnormal weight gain following exposure to high fat diets.
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Affiliation(s)
| | - Isabella Carucci
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | | | | | - Timothy J Jarome
- School of Animal Sciences, USA; School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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Minogue E, Cunha PP, Wadsworth BJ, Grice GL, Sah-Teli SK, Hughes R, Bargiela D, Quaranta A, Zurita J, Antrobus R, Velica P, Barbieri L, Wheelock CE, Koivunen P, Nathan JA, Foskolou IP, Johnson RS. Glutarate regulates T cell metabolism and anti-tumour immunity. Nat Metab 2023; 5:1747-1764. [PMID: 37605057 PMCID: PMC10590756 DOI: 10.1038/s42255-023-00855-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 07/03/2023] [Indexed: 08/23/2023]
Abstract
T cell function and fate can be influenced by several metabolites: in some cases, acting through enzymatic inhibition of α-ketoglutarate-dependent dioxygenases, in others, through post-translational modification of lysines in important targets. We show here that glutarate, a product of amino acid catabolism, has the capacity to do both, and has potent effects on T cell function and differentiation. We found that glutarate exerts those effects both through α-ketoglutarate-dependent dioxygenase inhibition, and through direct regulation of T cell metabolism via glutarylation of the pyruvate dehydrogenase E2 subunit. Administration of diethyl glutarate, a cell-permeable form of glutarate, alters CD8+ T cell differentiation and increases cytotoxicity against target cells. In vivo administration of the compound is correlated with increased levels of both peripheral and intratumoural cytotoxic CD8+ T cells. These results demonstrate that glutarate is an important regulator of T cell metabolism and differentiation with a potential role in the improvement of T cell immunotherapy.
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Affiliation(s)
- Eleanor Minogue
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Pedro P Cunha
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Brennan J Wadsworth
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Guinevere L Grice
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Shiv K Sah-Teli
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu Centre for Cell-Matrix Research, University of Oulu, Oulu, Finland
| | - Rob Hughes
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - David Bargiela
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Alessandro Quaranta
- Unit of Integrative Metabolomics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Javier Zurita
- Unit of Integrative Metabolomics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Pedro Velica
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Barbieri
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Craig E Wheelock
- Unit of Integrative Metabolomics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Respiratory Medicine and Allergy, Karolinska University Hospital, Stockholm, Sweden
| | - Peppi Koivunen
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu Centre for Cell-Matrix Research, University of Oulu, Oulu, Finland
| | - James A Nathan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Iosifina P Foskolou
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Randall S Johnson
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
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Snyder NW, Meier JL. Metabolic regulation of epigenetic drug resistance. Nat Chem Biol 2023; 19:1174-1175. [PMID: 37127755 DOI: 10.1038/s41589-023-01323-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Affiliation(s)
- Nathaniel W Snyder
- Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA.
| | - Jordan L Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, USA.
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Leveraging the secretory machinery to eliminate senescent cells. Nat Aging 2023; 3:1183-4. [PMID: 37709908 DOI: 10.1038/s43587-023-00500-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
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Dai Y, Ren D, He Y, Yi H. Editorial: Epigenetic, metabolic, and transcriptional regulation of immune cell plasticity and functions in cancer and non-cancer diseases. Front Immunol 2023; 14:1284124. [PMID: 37818355 PMCID: PMC10561278 DOI: 10.3389/fimmu.2023.1284124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 10/12/2023] Open
Affiliation(s)
- Yun Dai
- Laboratory of Cancer Precision Medicine, the First Hospital of Jilin University, Changchun, Jilin, China
| | - Dong Ren
- Irvine Medical Center, University of California, Irvine, Irvine, CA, United States
| | - Yafeng He
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Huanfa Yi
- Central Laboratory, the First Hospital of Jilin University, Changchun, Jilin, China
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